chr20-40464255-A-G

Variant names:

• chr20-40464255-A-G
• rs2143877
• XR_936718.3:n.1155+65T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_936718.3(LOC105372618):​n.1155+65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,176 control chromosomes in the GnomAD database, including 9,123 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (9123 hom., cov: 33)
• Consequence: LOC105372618 XR_936718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 10 publications found

Genes affected

LOC105372618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50685 AN: 152058 Hom.: 9109 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.298

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.333 AC: 50741 AN: 152176 Hom.: 9123 Cov.: 33 AF XY: 0.326 AC XY: 24244 AN XY: 74402

African (AFR) AF: 0.468 AC: 19429 AN: 41512

American (AMR) AF: 0.296 AC: 4524 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1401 AN: 5180

South Asian (SAS) AF: 0.321 AC: 1548 AN: 4824

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20218 AN: 67990

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.307 Hom.: 19205

Bravo AF: 0.345

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.052

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2143877; hg19: chr20-39092895;